Bob, to follow up on Annemarie and Rolf's discussion, under 'select' in the
manual, please add examples of insertion codes, with a comment that these
are "insertion codes" (so one can search for "insertion" and find it).
As stated, insertion codes are in column 27 of the PDB file.
An example is 1IGY chain B, where there are insertions at 52 (52 and 52^A)
and 82 (82, 82^A-82^C).
So, for example,
select 82:B # should select 4 residues
select 82^B:B # should select 1 residue
select 82^A:B-82^C:B # should select 3 residues, excluding 82
I say "should" because I have not tested these commands.
Chime note: Chime has no mechanism to include insertion codes in select
commands.
Thanks, -Eric
From: Rolf Huehne <[EMAIL PROTECTED]>
To: [email protected]
Subject: Re: [Jmol-users] Residue insertion nomenclature
Date: Thu, 19 Jan 2006 13:09:44 +0100
Annemarie Honegger wrote:
>
> Hi
>
> As I am trying to convert various chime/rasmol scripts to jmol, I am
> running into a problem:
> I am predominantly working with antibody structures, which usually
> use the Kabat convention
> for residue numbering in the PDB files, and thus rely on the residue
> insertion code, eg.
> Residue number 95a:L, 95b:L ..., 100a:H, 100b:H, 100c:H.. to identify
> the residues in
> the variable length loops of the different chains. These scripts
> fail in jmol, which appears not to understand residue
> numbers such as 100a or 100A. Is there any other way to access column
> 27 of the PDB record
> when specifying an atom/ residue selection in jmol?
>
Insertion codes are specified with a "^" sign, so in your example this
would be:
95^a:L, 95^b:L ..., 100^a:H, 100^b:H, 100^c:H
I am not sure when this was introduced, it works at least since
prerelease version 10.00.36.
Regards,
Rolf
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